GDAC_MergeDataFilesPipeline Execution Log 4:23 PM Mon Jul 2, '12

Running as user: cgaadm_deadline

GDAC_CreateMergeDataFilesSDRF1 samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.GBM.2012_06_23__00_00_19.samplestamp.txt
GDAC_CreateMergeDataFilesSDRF1 annotationid cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg
GDAC_CreateMergeDataFilesSDRF1 datapathsfile dependentsValues2163740715966570692.tsv
GDAC_MergeDataFiles2 inputfilelist filename dependentsValues7393232681965686004.tsv
GDAC_MergeDataFiles2 output filename GBM
GDAC_MergeDataFiles2 row_column row
GDAC_MergeDataFiles2 num_headers 1
GDAC_MergeDataFiles2 filetype cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg.seg
Execution Times:
Submitted: 16:23:24 02-07-12
Completed:
Elapsed: 00 hrs 00 mins 38 secs

step 1. GDAC_CreateMergeDataFilesSDRF [id: 118074] This module parses a samplestamp based on an input annotation id and creates an SDRF file as output.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00467:9
samplestamp file:/xchip/gdac_data/normalized/loadfiles/normalized/normalized.GBM.2012_06_23__00_00_19.samplestamp.txt
annotationid cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg
sdrffilename
datapathsfile dependentsValues2163740715966570692.tsv
Output Files:
 GBM.merger.sdrf.txt
 dcc_archive.properties
 .lsf.out
 dcc_archive_manifest.tsv
 stdout.txt
Execution Times:
Submitted: 16:23:24 02-07-12
Completed: 16:23:43 02-07-12
Elapsed: 00 hrs 00 mins 18 secs

step 2. GDAC_MergeDataFiles [id: 118075] Merges row or column oriented text datatable files, validating that the headers match.

    urn:lsid:broadinstitute.org:cancer.genome.analysis:00140:3
inputfilelist filename dependentsValues7393232681965686004.tsv
output filename GBM
row_column row
num_headers 1
filetype cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg.seg
Output Files:
 GBM.cna__hg_cgh_415k_g4124a__hms_harvard_edu__Level_3__segmentation__seg.seg.txt
 stdout.txt
Execution Times:
Submitted: 16:23:24 02-07-12
Completed: 16:23:59 02-07-12
Elapsed: 00 hrs 00 mins 34 secs